%LEAD_DISTANCES_LATEX Script to extract data on lead accuracy
%
% Provides data for latex reports.
%
% Usage: define target, STN, GPI, VIM
%
% Outputs: .mat & .csv file of distances + plots & coords
%
% NB: needs ea.stats open
% NNB: set for atlas Distal (medium)
%
% Michael Hart, University of British Columbia, August 2020
%LEAD_LOGBOOK Report on electrode accuracy (e.g. for a surgical logbook)
%
% Usage: define target, STN, GPI, VIM
% define "in" distance, distance considered inside the target
%
% Outputs: .mat & .csv file of distances + plots & coords
%
% NB: run from patient directory - needs ea.stats open
% NNB: all atlases are Distal (medium)
%
% Michael Hart, University of British Columbia, November 2020
%%lead_radar
%
% Script for analysing electrode targetting errors
%
% Just set group directory & target below
%
% NB: set for distal medium atlas
% NNB: saves & returns to group directory
%
% Michael Hart, University of British Columbia, December 2020
%LEAD_FLIPPER Duplicates leads for viewing single side results as a group
%
% Usage: subject to duplicate, absolute path
%
% Outputs: ea_reconstruction.mat in new lead_flipped folder within working directory
%
% NB: set for Medtronic 3389
%
% NNB: code based on discussion here
% [https://www.lead-dbs.org/forums/topic/export-code-for-vta-calculation/]
%
% Michael Hart, University of British Columbia, November 2020
=============================================================================================
tract_van.sh
(c) Michael Hart, University of British Columbia, August 2020
Function to run tractography on clinical DBS data (e.g. from UBC Functional Neurosurgery Programme)
Based on the following data: GE scanner, 3 Tesla, 32 Direction DTI protocol
Example:
tract_van.sh --data=diffusion.nii.gz --T1=mprage.nii.gz --bvecs=bvecs.txt --bvals=bvals.txt
Options:
Mandatory
--data diffusion data (e.g. standard = single B0 as first volume)
--T1 structural (T1) image
--bvecs bvecs file
--bvals bvals file
Optional
--acqparams acquisition parameters (custom values, for Eddy/TopUp)
--index diffusion PE directions (custom values, for Eddy/TopUp)
--segmentation additional segmentation template (for segmentation: standard is HarvardOxford)
--parcellation additional parcellation template (for connectomics: standard is HarvardOxford)
-d runs topup & eddy (see code for default acqparams/index parameters or enter custom as above)
-p parallel processing (slurm)*
-o overwrite
-h show this help
-v verbose
Pipeline
1. Baseline quality control
2. FSL_anat*
3. Freesurfer*
4. De-noising with topup & eddy - optional (see code)
5. FDT pipeline
6. BedPostX
7. Registration
8. XTRACT (including custom DBS tracts)
9. Segmentation (probtrackx2)
10. Connectomics (probtrackx2)
Version: 1.0
History: original
NB: requires Matlab, Freesurfer, FSL, ANTs, and set path to codedir
NNB: SGE / GPU acceleration - change eddy, bedpostx, probtrackx2, and XTRACT calls
=============================================================================================